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1. Tracked ultrasound registration for intraoperative navigation during pediatric bone tumor resections with soft tissue components: a porcine cadaver study

Author

van der Zee, J. M., Fitski, M., van de Sande, M. A. J., Buser, M. A. D., Hiep, M. A. J., Terwisscha van Scheltinga, C. E. J., Hulsker, C. C. C., van den Bosch, C. H., van de Ven, C. P., van der Heijden, L., Bökkerink, G. M. J., Wijnen, M. H. W. A., Siepel, F. J., and van der Steeg, A. F. W.

Published
2024
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3. The Significance of Hematuria in Podocytopathies

Author

Marchel, Dorota, Trachtman, Howard, Larkina, Maria, Helmuth, Margaret, Lai Yee, Jennifer Y., Fermin, Damian, Bomback, Andrew S., Canetta, Pietro A., Gipson, Debbie S., Mottl, Amy K., Parekh, Rulan S., Saha, Manish K., Sampson, Matthew G., Lafayette, Richard A., Mariani, Laura H., Massengill, S., Lo, L., Dell, K., Sedor, J., Martin, B., Lemley, K., Fajardo, C., Sharma, S., Srivastava, T., Markus, K., Sethna, C., Vento, S., Canetta, P., Pradhan, A., Gbadegesin, R., Olabisi, O., Smith, M., Greenbaum, L., Wang, C.S., Yun, E., Adler, S., LaPage, J., Amarah, A., Itteera, M., Atkinson, M., Williams, M., Fervenza, F., Hogan, M., Lieske, J., Selewski, D., Alston, C., Kaskel, F., Ross, M., Flynn, P., Kopp, J., Malaga-Dieguez, L., Zhdanova, O., Pehrson, L.J., Almaani, S., Roberts, L., Lafayette, R., Dave, S., Lee, I., Pfeffer, Z., Shah, S., Deslandes, A., Reich, H., Hladunewich, M., Ling, P., Romano, M., Brakeman, P, Podoll, A., Rogers, N., McCarthy, E., Landry, E., Fornoni, A., Bidot, C., Kretzler, M., Gipson, D., Williams, A., Stelzer, M., Nachman, P., Rheault, M., Rao, V., Derebail, V., Gibson, K., Froment, A., Ochoa-Toro, F., Holzman, L., Meyers, K., Kallem, K., Swenson, A., Sharma, K., Sambandam, K., Robles, E., Turk, M., Jefferson, A., Hingorani, S., Tuttle, K., Manahan, L., Pao, E., Kuykendall K, K., Lin, J.J., Cody, E., Kretzler, M., Barisoni, L., Gadegbeku, C., Gillespie, B., Gipson, D., Holzman, L., Mariani, L., Sampson, M.G., Sedor, J., Smith, A., Zee, J., Alter, G., Desmond, H., Eddy, S., Fermin, D., Ju, W., Larkina, M., Li, S., Lienczewski, C.C., Mainieri, T., Scherr, R., Troost, J., Williams, A., Wang, Y., Avila-Casado, Carmen, Bagnasco, Serena, Cassol, Clarissa, Bu, Lihong, Caltharp, Shelley, Demeke, Dawit, Gillespie, Brenda, Hassler, Jared, Herlitz, Leal, Hewitt, Stephen, Hodgin, Jeff, Holanda, Danni, Kambham, Neeraja, Lemley, Kevin, Mariani, Laura, Messias, Nidia, Mikhailov, Alexei, Najafian, Behzad, Palmer, Matthew, Rosenberg, Avi, Royal, Virginie, Stokes, Barry, Thomas, David, Yamashita, Michifumi, Yin, Hong, Zee, Jarcy, Zuo, Yiqin, Barisoni, Laura, Nast, Cynthia, Ahn, Wooin, Appel, Gerald, Appelbaum, Paul, Babayev, Revekka, Bomback, Andrew, Canetta, Pietro, Chan, Brenda, DʼAgati, Vivette Denise, Dogra, Samitri, Fernandez, Hilda, Gharavi, Ali, Hines, William, Husain, Syed Ali, Jain, Namrata, Kiryluk, Krzysztof, Lin, Fangming, Marasa, Maddalena, Markowitz, Glen, Rasouly, Hila Milo, Mohan, Sumit, Mongera, Nicola, Nestor, Jordan, Nickolas, Thomas, Radhakrishnan, Jai, Rao, Maya, Sanna-Cherchi, Simone, Shirazian, Shayan, Stokes, Michael Barry, Uy, Natalie, Valeri, Anthony, Vena, Natalie, Foroncewicz, Bartosz, Moszczuk, Barbara, Mucha, Krzysztof, Perkowska-Ptasińska, Agnieszka, Ghiggeri, Gian Marco, Lugani, Francesca, Ambruzs, Josephine, Liapis, Helen, Baracco, Rossana, Jain, Amrish, Ashoor, Isa, Aviles, Diego, Srivastava, Tarak, Ahn, Sun-Young, Devarajan, Prasad, Erkan, Elif, Claes, Donna, Stone, Hillarey, Mason, Sherene, Gbadegesin, Rasheed, Gomez-Mendez, Liliana, Greenbaum, Larry, Wang, Chia-shi, Yin, Hong (Julie), Cai, Yi, Jens, Goebel, Steinke, Julia, Weaver, Donald, Lane, Jerome, Cramer, Carl, Pan, Cindy, Paloian, Neil, Sreedharan, Rajasree, Selewski, David, Twombley, Katherine, Bowers, Corinna, Dreher, Mary, Kallash, Mahmoud, Mahan, John, Sharpe, Samantha, Smoyer, William, Al-Uzri, Amira, Iragorri, Sandra, Khalid, Myda, Belsha, Craig, Alge, Joseph, Braun, Michael, Gomez, AC, Wenderfer, Scott, Vasylyeva, Tetyana, Feig, Daniel, Fuentes, Gabriel Cara, Hannah, Melisha, Nester, Carla, Chishti, Aftab, Klein, Jon, Katsoufis, Chryso, Seeherunvong, Wacharee, Rheault, Michelle, Wong, Craig, Mathews, Nisha, Barcia, John, Swiatecka-Urban, Agnes, Bartosh, Sharon, Hunley, Tracy, Dharnidharka, Vikas, Gaut, Joseph, Laurin, Louis-Philippe, Royal, Virginie, Achanti, Anand, Budisavljevic, Milos, Self, Sally, Ghossein, Cybele, Peleg, Yonatan, Wadhwani, Shikha, Almaani, Salem, Ayoub, Isabelle, Nadasdy, Tibor, Samir, Parikh, Rovin, Brad, Chang, Anthony, Fatima, Huma, Julian, Bruce, Novak, Jan, Renfrow, Matthew, Rizk, Dana, Chen, Dhruti, Derebail, Vimal, Falk, Ronald, Gibson, Keisha, Glenn, Dorey, Hogan, Susan, Jain, Koyal, Jennette, J. Charles, Mottl, Amy, Poulton, Caroline, Saha, Manish Kanti, Fogo, Agnes, Sanghani, Neil, Kidd, Jason, Muthusamy, Selvaraj, Schelling, Jeffrey, Hou, Jean, Lemley, Kevin, Mika, Warren, Russo, Pierre, Denburg, Michelle, Kogon, Amy, Meyers, Kevin, Pradhan, Madhura, Matar, Raed Bou, OʼToole, John, Sedor, John, Sethna, Christine, Vento, Suzanne, Atta, Mohamed, Bagnasco, Serena, Neu, Alicia, Sperati, John, Adler, Sharon, Dai, Tiane, Dukkipati, Ram, Fervenza, Fernando, Sethi, Sanjeev, Kaskel, Frederick, Brathwaite, Kaye, Reidy, Kimberly, Weisstuch, Joseph, Wu, Ming, Zhdanova, Olga, Heymann, Jurgen, Kopp, Jeffrey, Waldman, Meryl, Winkler, Cheryl, Tuttle, Katherine, Krissberg, Jill, Lafayette, Richard, Fahmeedah, Kamal, Talley, Elizabeth, Hladunewich, Michelle, Parekh, Rulan, Avila-Casado, Carmen, Cattran, Daniel, Heather, Reich, Boll, Philip, Drexler, Yelena, Fornoni, Alessia, Gipson, Patrick, Hodgin, Jeffrey, Oliverio, Andrea, Hogan, Jon, Holzman, Lawrence, Palmer, Matthew, Coppock, Gaia, Abromovitz, Blaise, Mortiz, Michael, Alpers, Charles, Jefferson, J. Ashley, Brown, Elizabeth, Sambandam, Kamal, Roehm, Bethany, Smith, Abigail, Nast, Cynthia, Barisoni, Laura, Gillespie, Brenda, Robinson, Bruce, Kretzler, Matthias, Mariani, Laura, and Guay-Woodford, Lisa M.

Published
2024
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5. A glomerular transcriptomic landscape of apolipoprotein L1 in Black patients with focal segmental glomerulosclerosis

Author

Dell, K., Sedor, J., Schachere, M., Negrey, J., Lemley, K., Silesky, B., Srivastava, T., Garrett, A., Sethna, C., Laurent, K., Canetta, P., Pradhan, A., Greenbaum, L., Wang, C., Kang, C., Adler, S., LaPage, J., Athavale, A., Itteera, M., Atkinson, M., Dell, T., Fervenza, F., Hogan, M., Lieske, J., Chernitskiy, V., Kaskel, F., Ross, M., Flynn, P., Kopp, J., Blake, J., Trachtman, H., Zhdanova, O., Modersitzki, F., Vento, S., Lafayette, R., Mehta, K., Gadegbeku, C., Quinn-Boyle, S., Hladunewich, M., Reich, H., Ling, P., Romano, M., Fornoni, A., Bidot, C., Kretzler, M., Gipson, D., Williams, A., Klida, C., Derebail, V., Gibson, K., Cole, E., Ormond-Foster, J., Holzman, L., Meyers, K., Kallem, K., Swenson, A., Sambandam, K., Wang, Z., Rogers, M., Jefferson, A., Hingorani, S., Tuttle, K., Bray, M., Pao, E., Cooper, A., Lin, J.J., Baker, Stefanie, Barisoni, L., Bixler, J., Desmond, H., Eddy, S., Fermin, D., Gillespie, B., Kurtz, V., Larkina, M., Li, S., Lienczewski, C.C., Liu, J., Mainieri, T., Mariani, L., Sampson, M., Smith, A., Zee, J., Avila-Casado, Carmen, Bagnasco, Serena, Gaut, Joseph, Hewitt, Stephen, Hodgin, Jeff, Lemley, Kevin, Mariani, Laura, Palmer, Matthew, Rosenberg, Avi, Royal, Virginie, Thomas, David, Zee, Jarcy, Barisoni, Laura, Nast, Cynthia, McNulty, Michelle T., Fermin, Damian, Eichinger, Felix, Jang, Dongkeun, Kretzler, Matthias, Burtt, Noël P., Pollak, Martin R., Flannick, Jason, Weins, Astrid, Friedman, David J., and Sampson, Matthew G.

Published
2022
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6. Quantification of Glomerular Structural Lesions: Associations With Clinical Outcomes and Transcriptomic Profiles in Nephrotic Syndrome

Author

Dell, K., Sedor, J., Schachere, M., Negrey, J., Lemley, K., Lim, E., Srivastava, T., Garrett, A., Sethna, C., Laurent, K., Canetta, P., Pradhan, A., Greenbaum, L., Wang, C., Kang, C., Adler, S., LaPage, J., Athavale, A., Itteera, M., Atkinson, M., Boynton, S., Fervenza, F., Hogan, M., Lieske, J., Chernitskiy, V., Kaskel, F., Ross, M., Flynn, P., Kopp, J., Blake, J., Trachtman, H., Zhdanova, O., Modersitzki, F., Vento, S., Bray, M., Kelton, M., Cooper, A., Lafayette, R., Mehta, K., Gadegbeku, C., Quinn-Boyle, S., Hladunewich, M., Reich, H., Ling, P., Romano, M., Fornoni, A., Bidot, C., Kretzler, M., Gipson, D., Williams, A., LaVigne, J., Derebail, V., Gibson, K., Cole, E., Ormond-Foster, J., Holzman, L., Meyers, K., Kallem, K., Swenson, A., Sambandam, K., Wang, Z., Rogers, M., Jefferson, A., Hingorani, S., Tuttle, K., Lin, J.J., Barisoni, L., Bixler, J., Desmond, H., Eddy, S., Fermin, D., Gillespie, B., Kurtz, V., Larkina, M., Lavigne, J., Li, S., Lienczewski, C.C., Liu, J., Mainieri, T., Mariani, L., Sampson, M., Smith, A., Zee, J., Avila-Casado, Carmen, Bagnasco, Serena, Gaut, Joseph, Hewitt, Stephen, Hodgin, Jeff, Lemley, Kevin, Mariani, Laura, Palmer, Matthew, Rosenberg, Avi, Royal, Virginie, Thomas, David, Zee, Jarcy, Barisoni, Laura, Nast, Cynthia, Hodgin, Jeffrey B., Mariani, Laura H., Liu, Qian, Smith, Abigail R., Eddy, Sean, Hartman, John, Hamidi, Habib, Gaut, Joseph P., Palmer, Matthew B., Nast, Cynthia C., Chang, Anthony, Gillespie, Brenda W., Kretzler, Matthias, and Holzman, Lawrence B.

Published
2022
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7. Protein network analysis reveals selectively vulnerable regions and biological processes in FTD

Author

Bonham, Luke W, Steele, Natasha ZR, Karch, Celeste M, Manzoni, Claudia, Geier, Ethan G, Wen, Natalie, Ofori-Kuragu, Aaron, Momeni, Parastoo, Hardy, John, Miller, Zachary A, Hess, Christopher P, Lewis, Patrick, Miller, Bruce L, Seeley, William W, Baranzini, Sergio E, Desikan, Rahul S, Ferrari, Raffaele, Yokoyama, Jennifer S, Ferrari, R, Hernandez, DG, Nalls, MA, Rohrer, JD, Ramasamy, A, Kwok, JBJ, Dobson-Stone, C, Schofield, PR, Halliday, GM, Hodges, JR, Piguet, O, Bartley, L, Thompson, E, Hernández, I, Ruiz, A, Boada, M, Borroni, B, Padovani, A, Cruchaga, C, Cairns, NJ, Benussi, L, Binetti, G, Ghidoni, R, Forloni, G, Albani, D, Galimberti, D, Fenoglio, C, Serpente, M, Scarpini, E, Clarimón, J, Lleó, A, Blesa, R, Waldö, M Landqvist, Nilsson, K, Nilsson, C, Mackenzie, IRA, Hsiung, G-YR, Mann, D, Grafman, J, Morris, CM, Attems, J, Griffiths, TD, McKeith, IG, Thomas, AJ, Pietrini, P, Huey, ED, Wassermann, EM, Baborie, A, Jaros, E, Tierney, MC, Pastor, P, Razquin, C, Ortega-Cubero, S, Alonso, E, Perneczky, R, Diehl-Schmid, J, Alexopoulos, P, Kurz, A, Rainero, I, Rubino, E, Pinessi, L, Rogaeva, E, St George-Hyslop, P, Rossi, G, Tagliavini, F, Giaccone, G, Rowe, JB, Schlachetzki, JCM, Uphill, J, Collinge, J, Mead, S, Danek, A, Van Deerlin, VM, Grossman, M, Trojanowski, JQ, van der Zee, J, Van Broeckhoven, C, Cappa, SF, Leber, I, Hannequin, D, and Golfier, V

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Dementia, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Alzheimer's Disease Related Dementias (ADRD), Human Genome, Neurodegenerative, Rare Diseases, Frontotemporal Dementia (FTD), Biotechnology, Brain Disorders, Acquired Cognitive Impairment, Neurosciences, Aging, 2.1 Biological and endogenous factors, International FTD-Genomics Consortium, Clinical sciences
Abstract

ObjectiveThe neuroanatomical profile of behavioral variant frontotemporal dementia (bvFTD) suggests a common biological etiology of disease despite disparate pathologic causes; we investigated the genetic underpinnings of this selective regional vulnerability to identify new risk factors for bvFTD.MethodsWe used recently developed analytical techniques designed to address the limitations of genome-wide association studies to generate a protein interaction network of 63 bvFTD risk genes. We characterized this network using gene expression data from healthy and diseased human brain tissue, evaluating regional network expression patterns across the lifespan as well as the cell types and biological processes most affected in bvFTD.ResultsWe found that bvFTD network genes show enriched expression across the human lifespan in vulnerable neuronal populations, are implicated in cell signaling, cell cycle, immune function, and development, and are differentially expressed in pathologically confirmed frontotemporal lobar degeneration cases. Five of the genes highlighted by our differential expression analyses, BAIAP2, ERBB3, POU2F2, SMARCA2, and CDC37, appear to be novel bvFTD risk loci.ConclusionsOur findings suggest that the cumulative burden of common genetic variation in an interacting protein network expressed in specific brain regions across the lifespan may influence susceptibility to bvFTD.

Published
2018

9. Integrated care pathway for occupational pulmonary diseases.

Author

van der Valk, J. P. M., den Besten, L. A. A., Hylkema, T. H., van der Zee, J. S., Nijman, S. F. M., Van den Toorn, L. M., Braunstahl, G. J., in 't Veen, J. C. C. M., van Balen, P., Maas, J. J., Wennekes, R. H. A., de Groene, G. J., and Kappen, J. H.

Subjects
MEDICAL personnel, INDUSTRIAL nursing, HYPERSENSITIVITY pneumonitis, OCCUPATIONAL diseases, LUNG diseases, PULMONOLOGISTS
Abstract

The article discusses the development of an integrated care pathway for occupational pulmonary diseases, emphasizing the importance of early detection and collaboration between health care providers and occupational health professionals. The pathway consists of five steps, including medical consultation, occupational history assessment, diagnostic work-up, counseling, and follow-up. The ultimate goal is to ensure optimal prevention and care for work-related pulmonary diseases through collaboration among specialists and the registration of patient data in a national database. This Dutch model could serve as practical guidance for other countries aiming to optimize care for occupational pulmonary diseases. [Extracted from the article]

Published
2024
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11. Integrated care pathway for occupational pulmonary diseases

Author

van der Valk, J. P.M., den Besten, L. A.A., Hylkema, T. H., van der Zee, J. S., Nijman, S. F.M., Van den Toorn, L. M., Braunstahl, G. J., in ’t Veen, J. C.C.M., van Balen, P., Maas, J. J., Wennekes, R. H.A., de Groene, G. J., Kappen, J. H., van der Valk, J. P.M., den Besten, L. A.A., Hylkema, T. H., van der Zee, J. S., Nijman, S. F.M., Van den Toorn, L. M., Braunstahl, G. J., in ’t Veen, J. C.C.M., van Balen, P., Maas, J. J., Wennekes, R. H.A., de Groene, G. J., and Kappen, J. H.

Published
2024

14. Tracked ultrasound registration for intraoperative navigation during pediatric bone tumor resections with soft tissue components: a porcine cadaver study

Author

van der Zee, J. M., primary, Fitski, M., additional, van de Sande, M. A. J., additional, Buser, M. A. D., additional, Hiep, M. A. J., additional, Terwisscha van Scheltinga, C. E. J., additional, Hulsker, C. C. C., additional, van den Bosch, C. H., additional, van de Ven, C. P., additional, van der Heijden, L., additional, Bökkerink, G. M. J., additional, Wijnen, M. H. W. A., additional, Siepel, F. J., additional, and van der Steeg, A. F. W., additional

Published
2023
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20. Evaluating machine learning algorithms to Predict 30-day Unplanned REadmission (PURE) in Urology patients.

Author

Welvaars, Koen, van den Bekerom, Michel P. J., Doornberg, Job N., van Haarst, Ernst P., OLVG Urology Consortium, van der Zee, J. A., van Andel, G. A., Lagerveld, B. W., Hovius, M. C., Kauer, P. C., and Boevé, L. M. S.

Subjects
MACHINE learning, CLASSIFICATION algorithms, PATIENT readmissions, ADVERSE health care events, DISEASE risk factors, UROLOGY
Abstract

Background: Unplanned hospital readmissions are serious medical adverse events, stressful to patients, and expensive for hospitals. This study aims to develop a probability calculator to predict unplanned readmissions (PURE) within 30-days after discharge from the department of Urology, and evaluate the respective diagnostic performance characteristics of the PURE probability calculator developed with machine learning (ML) algorithms comparing regression versus classification algorithms. Methods: Eight ML models (i.e. logistic regression, LASSO regression, RIDGE regression, decision tree, bagged trees, boosted trees, XGBoost trees, RandomForest) were trained on 5.323 unique patients with 52 different features, and evaluated on diagnostic performance of PURE within 30 days of discharge from the department of Urology. Results: Our main findings were that performances from classification to regression algorithms had good AUC scores (0.62–0.82), and classification algorithms showed a stronger overall performance as compared to models trained with regression algorithms. Tuning the best model, XGBoost, resulted in an accuracy of 0.83, sensitivity of 0.86, specificity of 0.57, AUC of 0.81, PPV of 0.95, and a NPV of 0.31. Conclusions: Classification models showed stronger performance than regression models with reliable prediction for patients with high probability of readmission, and should be considered as first choice. The tuned XGBoost model shows performance that indicates safe clinical appliance for discharge management in order to prevent an unplanned readmission at the department of Urology. Plain Language Summary: Study need and importance: Unplanned readmissions form a consistent problem for many hospitals. Unplanned readmission rates can go up as high as to 35%, and may differ significantly between respective hospital departments. In addition, in the field of Urology readmission rates can be greatly influenced by type of surgery performed and unplanned readmissions in patients can go up as high as 26%. Although predicting unplanned readmissions for individual patients is often complex, due to multiple factors that need to be taken into account (e.g. functional disability, poor overall condition), there is evidence that these can be prevented when discharge management is evaluated with an objective measuring tool that facilitate such risk stratification between high and low risk patients. However, to the best of our knowledge, the latter risk stratification using ML driven probability calculators in the field of Urology have not been evaluated to date. Using ML, calculated risk scores based on analysing complex data patterns on patient level can support safe discharge and inform concerning the risk of having an unplanned readmission. What we found: Eight ML models were trained on 5.323 unique patients with 52 different features, and evaluated on diagnostic performance. Classification models showed stronger performance than regression models with reliable prediction for patients with high probability of readmission, and should be considered as first choice. The tuned XGBoost model shows performance that indicates safe clinical appliance for discharge management in order to prevent an unplanned readmission at the department of Urology. Limitations of our study were the quality and presence of patient data on features, and how to implement these findings in clinical setting to transition from predicting to preventing unplanned readmissions. Interpretation for clinicians: ML models based on classification should be first choice to predict unplanned readmissions, and the XGBoost model showed the strongest results. [ABSTRACT FROM AUTHOR]

Published
2023
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21. A glomerular transcriptomic landscape of apolipoprotein L1 in Black patients with focal segmental glomerulosclerosis

Author

McNulty, Michelle T., primary, Fermin, Damian, additional, Eichinger, Felix, additional, Jang, Dongkeun, additional, Kretzler, Matthias, additional, Burtt, Noël P., additional, Pollak, Martin R., additional, Flannick, Jason, additional, Weins, Astrid, additional, Friedman, David J., additional, Sampson, Matthew G., additional, Dell, K., additional, Sedor, J., additional, Schachere, M., additional, Negrey, J., additional, Lemley, K., additional, Silesky, B., additional, Srivastava, T., additional, Garrett, A., additional, Sethna, C., additional, Laurent, K., additional, Canetta, P., additional, Pradhan, A., additional, Greenbaum, L., additional, Wang, C., additional, Kang, C., additional, Adler, S., additional, LaPage, J., additional, Athavale, A., additional, Itteera, M., additional, Atkinson, M., additional, Dell, T., additional, Fervenza, F., additional, Hogan, M., additional, Lieske, J., additional, Chernitskiy, V., additional, Kaskel, F., additional, Ross, M., additional, Flynn, P., additional, Kopp, J., additional, Blake, J., additional, Trachtman, H., additional, Zhdanova, O., additional, Modersitzki, F., additional, Vento, S., additional, Lafayette, R., additional, Mehta, K., additional, Gadegbeku, C., additional, Quinn-Boyle, S., additional, Hladunewich, M., additional, Reich, H., additional, Ling, P., additional, Romano, M., additional, Fornoni, A., additional, Bidot, C., additional, Kretzler, M., additional, Gipson, D., additional, Williams, A., additional, Klida, C., additional, Derebail, V., additional, Gibson, K., additional, Cole, E., additional, Ormond-Foster, J., additional, Holzman, L., additional, Meyers, K., additional, Kallem, K., additional, Swenson, A., additional, Sambandam, K., additional, Wang, Z., additional, Rogers, M., additional, Jefferson, A., additional, Hingorani, S., additional, Tuttle, K., additional, Bray, M., additional, Pao, E., additional, Cooper, A., additional, Lin, J.J., additional, Baker, Stefanie, additional, Barisoni, L., additional, Bixler, J., additional, Desmond, H., additional, Eddy, S., additional, Fermin, D., additional, Gillespie, B., additional, Kurtz, V., additional, Larkina, M., additional, Li, S., additional, Lienczewski, C.C., additional, Liu, J., additional, Mainieri, T., additional, Mariani, L., additional, Sampson, M., additional, Smith, A., additional, Zee, J., additional, Avila-Casado, Carmen, additional, Bagnasco, Serena, additional, Gaut, Joseph, additional, Hewitt, Stephen, additional, Hodgin, Jeff, additional, Lemley, Kevin, additional, Mariani, Laura, additional, Palmer, Matthew, additional, Rosenberg, Avi, additional, Royal, Virginie, additional, Thomas, David, additional, Zee, Jarcy, additional, Barisoni, Laura, additional, and Nast, Cynthia, additional

Published
2022
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22. Quantification of Glomerular Structural Lesions: Associations With Clinical Outcomes and Transcriptomic Profiles in Nephrotic Syndrome

Author

Hodgin, Jeffrey B., primary, Mariani, Laura H., additional, Zee, Jarcy, additional, Liu, Qian, additional, Smith, Abigail R., additional, Eddy, Sean, additional, Hartman, John, additional, Hamidi, Habib, additional, Gaut, Joseph P., additional, Palmer, Matthew B., additional, Nast, Cynthia C., additional, Chang, Anthony, additional, Hewitt, Stephen, additional, Gillespie, Brenda W., additional, Kretzler, Matthias, additional, Holzman, Lawrence B., additional, Barisoni, Laura, additional, Dell, K., additional, Sedor, J., additional, Schachere, M., additional, Negrey, J., additional, Lemley, K., additional, Lim, E., additional, Srivastava, T., additional, Garrett, A., additional, Sethna, C., additional, Laurent, K., additional, Canetta, P., additional, Pradhan, A., additional, Greenbaum, L., additional, Wang, C., additional, Kang, C., additional, Adler, S., additional, LaPage, J., additional, Athavale, A., additional, Itteera, M., additional, Atkinson, M., additional, Boynton, S., additional, Fervenza, F., additional, Hogan, M., additional, Lieske, J., additional, Chernitskiy, V., additional, Kaskel, F., additional, Ross, M., additional, Flynn, P., additional, Kopp, J., additional, Blake, J., additional, Trachtman, H., additional, Zhdanova, O., additional, Modersitzki, F., additional, Vento, S., additional, Bray, M., additional, Kelton, M., additional, Cooper, A., additional, Lafayette, R., additional, Mehta, K., additional, Gadegbeku, C., additional, Quinn-Boyle, S., additional, Hladunewich, M., additional, Reich, H., additional, Ling, P., additional, Romano, M., additional, Fornoni, A., additional, Bidot, C., additional, Kretzler, M., additional, Gipson, D., additional, Williams, A., additional, LaVigne, J., additional, Derebail, V., additional, Gibson, K., additional, Cole, E., additional, Ormond-Foster, J., additional, Holzman, L., additional, Meyers, K., additional, Kallem, K., additional, Swenson, A., additional, Sambandam, K., additional, Wang, Z., additional, Rogers, M., additional, Jefferson, A., additional, Hingorani, S., additional, Tuttle, K., additional, Lin, J.J., additional, Barisoni, L., additional, Bixler, J., additional, Desmond, H., additional, Eddy, S., additional, Fermin, D., additional, Gillespie, B., additional, Kurtz, V., additional, Larkina, M., additional, Lavigne, J., additional, Li, S., additional, Lienczewski, C.C., additional, Liu, J., additional, Mainieri, T., additional, Mariani, L., additional, Sampson, M., additional, Smith, A., additional, Zee, J., additional, Avila-Casado, Carmen, additional, Bagnasco, Serena, additional, Gaut, Joseph, additional, Hodgin, Jeff, additional, Lemley, Kevin, additional, Mariani, Laura, additional, Palmer, Matthew, additional, Rosenberg, Avi, additional, Royal, Virginie, additional, Thomas, David, additional, and Nast, Cynthia, additional

Published
2022
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25. Choice-driven service network design for an integrated fixed line and demand responsive mobility system

Author

Sharif Azadeh, S. (author), van der Zee, J. (author), Wagenvoort, M. (author), Sharif Azadeh, S. (author), van der Zee, J. (author), and Wagenvoort, M. (author)

Abstract

Sparsely populated areas tend to be poorly served by Fixed Line and Schedule (FLS) public transport systems as the operation of a regular bus line is not economically viable for such areas. Therefore, introducing a Demand Responsive Transport (DRT) to partially replace FLS can result in increasing mobility service accessibility and inclusion. In this paper, a mixed-integer linear problem (MILP) is proposed to design an integrated FLS and DRT network for a transport operator. Passengers behavior is implicitly incorporated in our proposed approach via a discrete choice model. In addition, a tailored Adaptive Large Neighborhood Search (ALNS) coupled with tabu search and simulated annealing are introduced. We test our algorithm on real instances from a public transport operator in the Netherlands. The proposed algorithm can solve the problem up to 170 times faster than the MILP within 4% to 10% gap. Our proposed resolution approach investigates the temporal and spatial feasibility of deploying these integrated mobility systems based on the service level and provides recommendations to public transport operators., Transport and Planning

Published
2022
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27. ГИПЕРТЕРМИЯ В КОНСЕРВАТИВНОМ И ПАЛЛИАТИВНОМ ЛЕЧЕНИИ ОНКОЛОГИЧЕСКИХ БОЛЬНЫХ: ЧАСТЬ II. ОБЩАЯ ГИПЕРТЕРМИЯ

Author

Kurpeshev, O. K., van der Zee, J., and Surgery

Abstract

The analysis of the results of the use of whole-body hyperthermia (WBH) in patients with locally advanced, recurrent and / or metastatic tumors, which, as a rule, are radio- and chemo-resistant. Most patients were incurable, in connection with which the treatment was mainly carried out with a palliative purpose. The analysis showed that the method alone or in combination with chemo- and radiation therapy has pronounced direct and palliative effects, in some cases it provides long-term control. However, WBH can have side effects. This necessitates further improvement of the method, development of a set of preventive measures, as well as improvement of equipment for heating and thermometry.

Published
2022

28. Genetic architecture of sporadic frontotemporal dementia and overlap with Alzheimerʼs and Parkinsonʼs diseases

Author

Ferrari, Raffaele, Wang, Yunpeng, Vandrovcova, Jana, Guelfi, Sebastian, Witeolar, Aree, Karch, Celeste M, Schork, Andrew J, Fan, Chun C, Brewer, James B, Momeni, Parastoo, Schellenberg, Gerard D, Dillon, William P, Sugrue, Leo P, Hess, Christopher P, Yokoyama, Jennifer S, Bonham, Luke W, Rabinovici, Gil D, Miller, Bruce L, Andreassen, Ole A, Dale, Anders M, Hardy, John, Desikan, Rahul S, Hernandez, D G, Nalls, M A, Rohrer, J D, Ramasamy, A, Kwok, J B J, Dobson-Stone, C, Schofield, P R, Halliday, G M, Hodges, J R, Piguet, O, Bartley, L, Thompson, E, Haan, E, Hernández, I, Ruiz, A, Boada, M, Borroni, B, Padovani, A, Cruchaga, C, Cairns, N J, Benussi, L, Binetti, G, Ghidoni, R, Forloni, G, Albani, D, Galimberti, D, Fenoglio, C, Serpente, M, Scarpini, E, Clarimón, J, Lleó, A, Blesa, R, Landqvist Waldö, M, Nilsson, K, Nilsson, C, Mackenzie, I R A, Hsiung, G-Y R, Mann, D M A, Grafman, J, Morris, C M, Attems, J, Griffiths, T D, McKeith, I G, Thomas, A J, Pietrini, P, Huey, E D, Wassermann, E M, Baborie, A, Jaros, E, Tierney, M C, Pastor, P, Razquin, C, Ortega-Cubero, S, Alonso, E, Perneczky, R, Diehl-Schmid, J, Alexopoulos, P, Kurz, A, Rainero, I, Rubino, E, Pinessi, L, Rogaeva, E, St George-Hyslop, P, Rossi, G, Tagliavini, F, Giaccone, G, Rowe, J B, Schlachetzki, J C M, Uphill, J, Collinge, J, Mead, S, Danek, A, Van Deerlin, V M, Grossman, M, Trojanowski, J Q, van der Zee, J, Cruts, M, Van Broeckhoven, C, Cappa, S F, Leber, I, Hannequin, D, Golfier, V, Vercelletto, M, Brice, A, Nacmias, B, Sorbi, S, Bagnoli, S, Piaceri, I, Nielsen, J E, Hjermind, L E, Riemenschneider, M, Mayhaus, M, Ibach, B, Gasparoni, G, Pichler, S, Gu, W, Rossor, M N, Fox, N C, Warren, J D, Spillantini, M G, Morris, H R, Rizzu, P, Heutink, P, Snowden, J S, Rollinson, S, Richardson, A, Gerhard, A, Bruni, A C, Maletta, R, Frangipane, F, Cupidi, C, Bernardi, L, Anfossi, M, Gallo, M, Conidi, M E, Smirne, N, Rademakers, R, Baker, M, Dickson, D W, Graff-Radford, N R, Petersen, R C, Knopman, D, Josephs, K A, Boeve, B F, Parisi, J E, Seeley, W W, Karydas, A M, Rosen, H, van Swieten, J C, Dopper, E G P, Seelaar, H, Pijnenburg, Y A L, Scheltens, P, Logroscino, G, Capozzo, R, Novelli, V, Puca, A A, Franceschi, M, Postiglione, A, Milan, G, Sorrentino, P, Kristiansen, M, Chiang, H-H, Graff, C, Pasquier, F, Rollin, A, Deramecourt, V, Lebouvier, T, Kapogiannis, D, Ferrucci, L, Pickering-Brown, S, and Singleton, A B

Published
2017
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29. LifeTime and improving European healthcare through cell-based interceptive medicine

Author

Rajewsky, N., Almouzni, G., Gorski, S., Aerts, S., Amit, I., Bertero, M., Bock, C., Bredenoord, A., Cavalli, G., Chiocca, S., Clevers, H., Strooper, B., Eggert, A., Ellenberg, J., Fernández, X., Figlerowicz, M., Gasser, S., Hubner, N., Kjems, J., Knoblich, J., Krabbe, G., Lichter, P., Linnarsson, S., Marine, J., Marioni, J., Marti-Renom, M., Netea, M., Nickel, D., Nollmann, M., Novak, H., Parkinson, H., Piccolo, S., Pinheiro, I., Pombo, A., Popp, C., Reik, W., Roman-Roman, S., Rosenstiel, P., Schultze, J., Stegle, O., Tanay, A., Testa, G., Thanos, D., Theis, F., Torres-Padilla, M., Valencia, A., Vallot, C., van Oudenaarden, A., Vidal, M., Voet, T., Alberi, L., Alexander, S., Alexandrov, T., Arenas, E., Bagni, C., Balderas, R., Bandelli, A., Becher, B., Becker, M., Beerenwinkel, N., Benkirame, M., Beyer, M., Bickmore, W., Biessen, E., Blomberg, N., Blumcke, I., Bodenmiller, B., Borroni, B., Boumpas, D., Bourgeron, T., Bowers, S., Braeken, D., Brooksbank, C., Brose, N., Bruining, H., Bury, J., Caporale, N., Cattoretti, G., Chabane, N., Chneiweiss, H., Cook, S., Curatolo, P., de Jonge, M., Deplancke, B., de Witte, P., Dimmeler, S., Draganski, B., Drews, A., Dumbrava, C., Engelhardt, S., Gasser, T., Giamarellos-Bourboulis, E., Graff, C., Grün, D., Gut, I., Hansson, O., Henshall, D., Herland, A., Heutink, P., Heymans, S., Heyn, H., Huch, M., Huitinga, I., Jackowiak, P., Jongsma, K., Journot, L., Junker, J., Katz, S., Kehren, J., Kempa, S., Kirchhof, P., Klein, C., Koralewska, N., Korbel, J., Kühnemund, M., Lamond, A., Lauwers, E., Le Ber, I., Leinonen, V., Tobon, A., Lundberg, E., Lunkes, A., Maatz, H., Mann, M., Marelli, L., Matser, V., Matthews, P., Mechta-Grigoriou, F., Menon, R., Nielsen, A., Pagani, M., Pasterkamp, R., Pitkänen, A., Popescu, V., Pottier, C., Puisieux, A., Rademakers, R., Reiling, D., Reiner, O., Remondini, D., Ritchie, C., Rohrer, J., Saliba, A., Sanchez-Valle, R., Santosuosso, A., Sauter, A., Scheltema, R., Scheltens, P., Schiller, H., Schneider, A., Seibler, P., Sheehan-Rooney, K., Shields, D., Sleegers, K., Smit, A., Smith, K., Smolders, I., Synofzik, M., Tam, W., Teichmann, S., Thom, M., Turco, M., van Beusekom, H., Vandenberghe, R., den Hoecke, S., de Poel, I., van der Ven, A., van der Zee, J., van Lunzen, J., van Minnebruggen, G., Paesschen, W., van Swieten, J., van Vught, R., Verhage, M., Verstreken, P., Villa, C., Vogel, J., von Kalle, C., Walter, J., Weckhuysen, S., Weichert, W., Wood, L., Ziegler, A., Zipp, F., HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany., Medical Research Council (MRC), UK DRI Ltd, TWINCORE, Zentrum für experimentelle und klinische Infektionsforschung GmbH,Feodor-Lynen Str. 7, 30625 Hannover, Germany., Barcelona Supercomputing Center, LifeTime Community Working Groups, Cardiology, Neurology, Institut de génétique humaine (IGH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Amsterdam Neuroscience - Cellular & Molecular Mechanisms, Human genetics, Rajewsky N., Almouzni G., Gorski S.A., Aerts S., Amit I., Bertero M.G., Bock C., Bredenoord A.L., Cavalli G., Chiocca S., Clevers H., De Strooper B., Eggert A., Ellenberg J., Fernandez X.M., Figlerowicz M., Gasser S.M., Hubner N., Kjems J., Knoblich J.A., Krabbe G., Lichter P., Linnarsson S., Marine J.-C., Marioni J.C., Marti-Renom M.A., Netea M.G., Nickel D., Nollmann M., Novak H.R., Parkinson H., Piccolo S., Pinheiro I., Pombo A., Popp C., Reik W., Roman-Roman S., Rosenstiel P., Schultze J.L., Stegle O., Tanay A., Testa G., Thanos D., Theis F.J., Torres-Padilla M.-E., Valencia A., Vallot C., van Oudenaarden A., Vidal M., Voet T., Alberi L., Alexander S., Alexandrov T., Arenas E., Bagni C., Balderas R., Bandelli A., Becher B., Becker M., Beerenwinkel N., Benkirame M., Beyer M., Bickmore W., Biessen E.E.A.L., Blomberg N., Blumcke I., Bodenmiller B., Borroni B., Boumpas D.T., Bourgeron T., Bowers S., Braeken D., Brooksbank C., Brose N., Bruining H., Bury J., Caporale N., Cattoretti G., Chabane N., Chneiweiss H., Cook S.A., Curatolo P., de Jonge M.I., Deplancke B., de Witte P., Dimmeler S., Draganski B., Drews A., Dumbrava C., Engelhardt S., Gasser T., Giamarellos-Bourboulis E.J., Graff C., Grun D., Gut I., Hansson O., Henshall D.C., Herland A., Heutink P., Heymans S.R.B., Heyn H., Huch M., Huitinga I., Jackowiak P., Jongsma K.R., Journot L., Junker J.P., Katz S., Kehren J., Kempa S., Kirchhof P., Klein C., Koralewska N., Korbel J.O., Kuhnemund M., Lamond A.I., Lauwers E., Le Ber I., Leinonen V., Tobon A.L., Lundberg E., Lunkes A., Maatz H., Mann M., Marelli L., Matser V., Matthews P.M., Mechta-Grigoriou F., Menon R., Nielsen A.F., Pagani M., Pasterkamp R.J., Pitkanen A., Popescu V., Pottier C., Puisieux A., Rademakers R., Reiling D., Reiner O., Remondini D., Ritchie C., Rohrer J.D., Saliba A.-E., Sanchez-Valle R., Santosuosso A., Sauter A., Scheltema R.A., Scheltens P., Schiller H.B., Schneider A., Seibler P., Sheehan-Rooney K., Shields D., Sleegers K., Smit A.B., Smith K.G.C., Smolders I., Synofzik M., Tam W.L., Teichmann S., Thom M., Turco M.Y., van Beusekom H.M.M., Vandenberghe R., Van den Hoecke S., Van de Poel I., van der Ven A., van der Zee J., van Lunzen J., van Minnebruggen G., Van Paesschen W., van Swieten J., van Vught R., Verhage M., Verstreken P., Villa C.E., Vogel J., von Kalle C., Walter J., Weckhuysen S., Weichert W., Wood L., Ziegler A.-G., Zipp F., Center for Neurogenomics and Cognitive Research, Functional Genomics, Rajewsky, N, Almouzni, G, Gorski, S, Aerts, S, Amit, I, Bertero, M, Bock, C, Bredenoord, A, Cavalli, G, Chiocca, S, Clevers, H, De Strooper, B, Eggert, A, Ellenberg, J, Fernández, X, Figlerowicz, M, Gasser, S, Hubner, N, Kjems, J, Knoblich, J, Krabbe, G, Lichter, P, Linnarsson, S, Marine, J, Marioni, J, Marti-Renom, M, Netea, M, Nickel, D, Nollmann, M, Novak, H, Parkinson, H, Piccolo, S, Pinheiro, I, Pombo, A, Popp, C, Reik, W, Roman-Roman, S, Rosenstiel, P, Schultze, J, Stegle, O, Tanay, A, Testa, G, Thanos, D, Theis, F, Torres-Padilla, M, Valencia, A, Vallot, C, van Oudenaarden, A, Vidal, M, Voet, T, Cattoretti, G, Alliance for Modulation in Epilepsy, Pharmaceutical and Pharmacological Sciences, Experimental Pharmacology, RS: Carim - H02 Cardiomyopathy, MUMC+: MA Med Staf Spec Cardiologie (9), and Cardiologie

Subjects
0301 basic medicine, Male, Artificial intelligence, Legislation, Medical, [SDV]Life Sciences [q-bio], Molecular datasets, lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], Cell- and Tissue-Based Therapy, Diseases, LifeTime Community Working Groups, Disease, Biomarkers, Systems biology, Health data, Pharmacology, Toxicology and Pharmaceutics(all), 0302 clinical medicine, Conjunts de dades, ethics [Delivery of Health Care], Health care, Pathology, Medicine, European healthcare, BRAIN, Single-cell multi-omics, GENE-EXPRESSION, Multidisciplinary, methods [Medicine], Education, Medical, Settore BIO/13, Intel.ligència artificial, 3. Good health, ALZHEIMERS-DISEASE, Europe, Health, Management system, Perspective, Female, ddc:500, Single-Cell Analysis, Biomarkers, Diseases, Systems biology, Complex diseases, Informàtica::Aplicacions de la informàtica::Bioinformàtica [Àrees temàtiques de la UPC], medicine.medical_specialty, General Science & Technology, Cells, MEDLINE, cell-based interceptive medicine, LifeTime Initiative, 03 medical and health sciences, SDG 3 - Good Health and Well-being, Clinical datasets, Artificial Intelligence, REVEALS, LifeTime Community, standards [Medicine], Humans, OMICS, RECONSTRUCTION, Intensive care medicine, trends [Medicine], trends [Delivery of Health Care], business.industry, Disease progression, standards [Delivery of Health Care], methods [Delivery of Health Care], 030104 developmental biology, lnfectious Diseases and Global Health Radboud Institute for Health Sciences [Radboudumc 4], single cell, personalized therapy, machine learning, bioinformatics, systems biology, disease, cell-based interceptive medicine, Early Diagnosis, Cardiovascular and Metabolic Diseases, Human medicine, business, Delivery of Health Care, 030217 neurology & neurosurgery, Cell based
Abstract

Here we describe the LifeTime Initiative, which aims to track, understand and target human cells during the onset and progression of complex diseases, and to analyse their response to therapy at single-cell resolution. This mission will be implemented through the development, integration and application of single-cell multi-omics and imaging, artificial intelligence and patient-derived experimental disease models during the progression from health to disease. The analysis of large molecular and clinical datasets will identify molecular mechanisms, create predictive computational models of disease progression, and reveal new drug targets and therapies. The timely detection and interception of disease embedded in an ethical and patient-centred vision will be achieved through interactions across academia, hospitals, patient associations, health data management systems and industry. The application of this strategy to key medical challenges in cancer, neurological and neuropsychiatric disorders, and infectious, chronic inflammatory and cardiovascular diseases at the single-cell level will usher in cell-based interceptive medicine in Europe over the next decade., The LifeTime initiative is an ambitious, multidisciplinary programme that aims to improve healthcare by tracking individual human cells during disease processes and responses to treatment in order to develop and implement cell-based interceptive medicine in Europe.

Published
2020
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37. Hyperthermia for deep seated tumours – possibilities of heating with capacitive devices

Author

Marta Cavagnaro, J. van der Zee J. van der Zee, O. Kurpeshev, and Radiation Oncology

Subjects
electromagnetic fields, Hyperthermia, capacitive devices, business.industry, Capacitive sensing, thermochemoradiation therapy, radiation therapy, chemotherapy, thermoradiotherapy, thermochemotherapy, hyperthermia, medicine.disease, 030218 nuclear medicine & medical imaging, 03 medical and health sciences, 0302 clinical medicine, Nuclear Energy and Engineering, 030220 oncology & carcinogenesis, medicine, business, Biomedical engineering
Abstract

The review examines the general principles of capacitive electromagnetic hyperthermia (EMHT), the distribution of electromagnetic energy in various experimental models and in patients’ tumors, the design features of applicators from various capacitive hyperthermic systems and their role in achieving hyperthermic mode in tumors of deep localization. In classical capacitive EMHT, the main obstacle in achieving the required temperature in such tumors is overheating of the subcutaneous fatty tissue under the electrodes. For some capacitive hyperthermic systems, the heating of adipose tissues is enhanced due to the fact that the applicator design does not conform to certain technical requirements. In capacitive EMHT at frequencies of 8–13.56 MHz, obtaining the minimum hyperthermic mode is possible with output powers of 500–800 W, maximum – 1000–1200 W and above. The results of the use of various hyperthermic capacitive systems in patients with malignant tumors of internal organs are analyzed.

Published
2019
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42. Extensive genetic and phenotypic description of MAPT p.R406W in the Flanders-Belgian population

Author

Gossye, H., Van Mossevelde, S., Van Der Zee, J., Vermeiren, Y., De Roeck, N., Sieben, A., De Bleecker, J., De Deyn, P., Cras, P., Engelborghs, S., Van Broeckhoven, C., Neurology, Physiotherapy, Human Physiology and Anatomy, Clinical sciences, and Neuroprotection & Neuromodulation

Subjects
Genetic, Belgium, Neuroscience(all), neurology, MAPT p.R406W, Phenotypic Description, Flanders
Published
2021

44. Kidney Biopsy Features Most Predictive of Clinical Outcomes in the Spectrum of Minimal Change Disease and Focal Segmental Glomerulosclerosis

Author

Zee, Jarcy, Liu, Qian, Smith, Abigail R., Hodgin, Jeffrey B., Rosenberg, Avi, Gillespie, Brenda W., Holzman, Lawrence B., Barisoni, Laura, Mariani, Laura H., Adler, S., Alter, G., Athavale, A., Atkinson, M., Avila-Casado, C., Bagnasco, S., Baker, S., Barisoni, L., Bidot, C., Blake, J., Bray, M., Canetta, P., Chernitskiy, V., Cooper, A., Dell, K., Dell, T., Derebail, V., Desmond, H., Eddy, S., Fermin, D., Fervenza, F., Flynn, P., Fornoni, A., Froment, A., Gadegbeku, C., Gaut, J., Gibson, K., Gillespie, B., Gipson, D., Greenbaum, L., Hewitt, S., Hingorani, S., Hladunewich, M., Hodgin, J., Hogan, M., Holzman, L., Itteera, M., Jefferson, A., Kallem, K., Kaskel, F., Klida, C., Kretzler, M., Kopp, J., Kretzler, M., Kurtz, V., Lafayette, R., LaPage, J., Larkina, M., Lemley, K., Lieske, J., Li, S., Li, S., Lienczewski, C.C., Lin, J.J., Ling, P., Liu, J., Mainieri, T., Mariani, L., Meyers, K., Modersitzki, F., Morrison, S., Nast, C., Negrey, J., Ormond-Foster, J., Palmer, M., Pao, E., Pfaiff, M., Pradhan, A., Romano, M., Rosenberg, A., Royal, V., Quinn-Boyle, S., Reich, H., Rogers, M., Ross, M., Sambandam, K., Sampson, M., Schachere, M., Sedor, J., Sethna, C., Srivastava, T., Smith, A., Swenson, A., Tang, S., Thomas, D., Trachtman, H., Tuttle, K., Vento, S., Wang, C., Wang, Z., Williams, A., Yeung, B., Yun, E., Zee, J., Zhdanova, O., Adler, S., Alter, G., Athavale, A., Atkinson, M., Avila-Casado, C., Bagnasco, S., Baker, S., Barisoni, L., Bidot, C., Blake, J., Bray, M., Canetta, P., Cassol, C., Chernitskiy, V., Cooper, A., Dell, K., Dell, T., Demeke, D., Derebail, V., Desmond, H., Eddy, S., Fermin, D., Fervenza, F., Flynn, P., Fornoni, A., Froment, A., Gadegbeku, C., Gaut, J., Gibson, K., Gillespie, B., Gipson, D., Greenbaum, L., Hewitt, S., Hingorani, S., Hladunewich, M., Hodgin, J., Hogan, M., Holanda, D., Holzman, L., Itteera, M., Jefferson, A., Kallem, K., Kaskel, F., Klida, C., Kopp, J., Kretzler, M., Kurtz, V., Lafayette, R., LaPage, J., Larkina, M., Lemley, K., Lieske, J., Li, S., Li, S., Lienczewski, C.C., Lin, J.J., Ling, P., Liu, J., Mainieri, T., Mariani, L., Messias, N., Meyers, K., Michailov, A., Modersitzki, F., Morrison, S., Nast, C., Negrey, J., Ormond-Foster, J., Palmer, M., Pao, E., Pfaiff, M., Pradhan, A., Romano, M., Rosenberg, A., Royal, V., Quinn-Boyle, S., Reich, H., Rogers, M., Ross, M., Sambandam, K., Sampson, M., Schachere, M., Sedor, J., Sethna, C., Srivastava, T., Smith, A., Swenson, A., Tang, S., Thomas, D., Trachtman, H., Tuttle, K., Vento, S., Wang, C., Wang, Z., Williams, A., Yamashita, M., Yeung, B., Yun, E., Zee, J., Zhdanova, O., and Zuo, Y.

Abstract

The classification of podocytopathies, including minimal change disease (MCD) and focal segmental glomerulosclerosis (FSGS), has historically been based on limited glomerular features. This study used supervised machine learning methods to identify the most important clinical and histopathologic predictors of disease progression, complete proteinuria remission, and treatment response in MCD/FSGS. The top predictors included conventional and novel glomerular and tubulointerstitial features. Biopsy reporting for podocytopathies should be standardized by including these prognostic morphologic features to inform risk stratification.

Published
2022
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47. A C6orf10/LOC101929163 locus is associated with age of onset in C9orf72 carriers

Author

Zhang M1, 2 3, Ferrari R4, Tartaglia MC3, 5 6, Keith J7, Surace EI8, Wolf U9, Sato C3, Grinberg M3, Liang Y3, Xi Z3, Dupont K3, McGoldrick P3, Weichert A3, McKeever PM3, Schneider R3, 6 7, McCorkindale MD4, Manzoni C10, Rademakers R11, Graff-Radford NR12, Dickson DW11, Parisi JE13, Boeve BF14, Petersen RC14, Miller BL15, Seeley WW16, van Swieten JC17, van Rooij J17, Pijnenburg Y18, van der Zee J19, Van Broeckhoven C19, Le Ber I21, Van Deerlin V23, Suh E23, Rohrer JD24, Mead S25, Graff C26, Öijerstedt L26, Pickering-Brown S28, Rollinson S28, Rossi G29, Tagliavini F30, Brooks WS31, Dobson-Stone C32, Halliday GM32, Hodges JR32, Piguet O34, Binetti G36, Benussi L37, Ghidoni R37, Nacmias B38, Sorbi S38, Bruni AC40, Galimberti D41, Scarpini E41, Rainero I42, Rubino E42, Clarimon J43, Lleó A43, Ruiz A45, Hernández I45, Pastor P46, Diez-Fairen M46, Borroni B48, Pasquier F49, Deramecourt V49, Lebouvier T49, Perneczky R50, 51 52, Diehl-Schmid J50, Grafman J53, Huey ED55, Mayeux R55, Nalls MA57, Hernandez D57, Singleton A57, Momeni P58, Zeng Z59, Hardy J4, Robertson J3, Zinman L6, 7, Rogaeva E3, 6, International FTD-Genomics Consortium (IFGC), Ferrari R, Hernandez DG, Nalls MA, Rohrer JD, Ramasamy A, Kwok JBJ, Dobson-Stone C, Brooks WS, Schofield PR, Halliday GM, Hodges JR, Piguet O, Bartley L, Thompson E, Hernández I, Ruiz A, Boada M, Borroni B, Padovani A, Cruchaga C, Cairns NJ, Benussi L, Binetti G, Ghidoni R, Forloni G, Albani D, Galimberti D, Fenoglio C, Serpente M, Scarpini E, Clarimón J, Lleó A, Blesa R, Wald Ouml ML, Nilsson K, Nilsson C, Mackenzie IRA, Hsiung GR, Mann DMA, Grafman J, Morris CM, Attems J, Griffiths TD, McKeith IG, Thomas AJ, Pietrini P, Huey ED, Wassermann EM, Baborie A, Jaros E, Tierney MC, Pastor P, Razquin C, Ortega-Cubero S, Alonso E, Perneczky R, Diehl-Schmid J, Alexopoulos P, Kurz A, Rainero I, Rubino E, Pinessi L, Rogaeva E, St George-Hyslop P, Rossi G, Tagliavini F, Giaccone G, Rowe JB, Schlachetzki JCM, Uphill J, Collinge J, Mead S, Danek A, Van Deerlin VM, Grossman M, Trojanowski JQ, van der Zee J, Van Broeckhoven C, Cappa SF, Leber I, Hannequin D, Golfier V, Vercelletto M, Brice A, Nacmias B, Sorbi S, Bagnoli S, Piaceri I, Nielsen JE, Hjermind LE, Riemenschneider M, Mayhaus M, Ibach B, Gasparoni G, Pichler S, Gu W, Rossor MN, Fox NC, Warren JD, Grazia Spillantini M, Morris HR, Rizzu P, Heutink P, Snowden JS, Rollinson S, Richardson A, Gerhard A, Bruni AC, Maletta R, Frangipane F, Cupidi C, Bernardi L, Anfossi M, Gallo M, Elena Conidi M, Smirne N, Rademakers R, Baker M, Dickson DW, Graff-Radford NR, Petersen RC, Knopman D, Josephs KA, Boeve BF, Parisi JE, Seeley WW, Miller BL, Karydas AM, Rosen H, van Swieten JC, Dopper EGP, Seelaar H, Pijnenburg YAL, Scheltens P, Logroscino G, Capozzo R, Novelli V, Puca AA, Franceschi M, Postiglione A, Milan G, Sorrentino P, Kristiansen M, Chiang HH, Graff C, Pasquier F, Rollin A, Deramecourt V, Lebouvier T, Kapogiannis D, Ferrucci L, Pickering-Brown S, Singleton AB, Hardy J, Momeni P, Human genetics, Amsterdam Neuroscience - Neurodegeneration, Neurology, Divisions, Zhang, M1, 2, 3, Ferrari, R4, Tartaglia, Mc3, 5, 6, Keith, J7, Surace, Ei8, Wolf, U9, Sato, C3, Grinberg, M3, Liang, Y3, Xi, Z3, Dupont, K3, Mcgoldrick, P3, Weichert, A3, Mckeever, Pm3, Schneider, R3, 6, 7, Mccorkindale, Md4, Manzoni, C10, Rademakers, R11, Graff-Radford, Nr12, Dickson, Dw11, Parisi, Je13, Boeve, Bf14, Petersen, Rc14, Miller, Bl15, Seeley, Ww16, van Swieten, Jc17, van Rooij, J17, Pijnenburg, Y18, van der Zee, J19, Van Broeckhoven, C19, Le Ber, I21, Van Deerlin, V23, Suh, E23, Rohrer, Jd24, Mead, S25, Graff, C26, Öijerstedt, L26, Pickering-Brown, S28, Rollinson, S28, Rossi, G29, Tagliavini, F30, Brooks, Ws31, Dobson-Stone, C32, Halliday, Gm32, Hodges, Jr32, Piguet, O34, Binetti, G36, Benussi, L37, Ghidoni, R37, Nacmias, B38, Sorbi, S38, Bruni, Ac40, Galimberti, D41, Scarpini, E41, Rainero, I42, Rubino, E42, Clarimon, J43, Lleó, A43, Ruiz, A45, Hernández, I45, Pastor, P46, Diez-Fairen, M46, Borroni, B48, Pasquier, F49, Deramecourt, V49, Lebouvier, T49, Perneczky, R50, 51, 52, Diehl-Schmid, J50, Grafman, J53, Huey, Ed55, Mayeux, R55, Nalls, Ma57, Hernandez, D57, Singleton, A57, Momeni, P58, Zeng, Z59, Hardy, J4, Robertson, J3, Zinman, L6, Rogaeva, E3, International FTD-Genomics Consortium, (IFGC), Ferrari, R, Hernandez, Dg, Nalls, Ma, Rohrer, Jd, Ramasamy, A, Kwok, Jbj, Dobson-Stone, C, Brooks, W, Schofield, Pr, Halliday, Gm, Hodges, Jr, Piguet, O, Bartley, L, Thompson, E, Hernández, I, Ruiz, A, Boada, M, Borroni, B, Padovani, A, Cruchaga, C, Cairns, Nj, Benussi, L, Binetti, G, Ghidoni, R, Forloni, G, Albani, D, Galimberti, D, Fenoglio, C, Serpente, M, Scarpini, E, Clarimón, J, Lleó, A, Blesa, R, Wald Ouml, Ml, Nilsson, K, Nilsson, C, Mackenzie, Ira, Hsiung, Gr, Mann, Dma, Grafman, J, Morris, Cm, Attems, J, Griffiths, Td, Mckeith, Ig, Thomas, Aj, Pietrini, P, Huey, Ed, Wassermann, Em, Baborie, A, Jaros, E, Tierney, Mc, Pastor, P, Razquin, C, Ortega-Cubero, S, Alonso, E, Perneczky, R, Diehl-Schmid, J, Alexopoulos, P, Kurz, A, Rainero, I, Rubino, E, Pinessi, L, Rogaeva, E, St George-Hyslop, P, Rossi, G, Tagliavini, F, Giaccone, G, Rowe, Jb, Schlachetzki, Jcm, Uphill, J, Collinge, J, Mead, S, Danek, A, Van Deerlin, Vm, Grossman, M, Trojanowski, Jq, van der Zee, J, Van Broeckhoven, C, Cappa, Sf, Leber, I, Hannequin, D, Golfier, V, Vercelletto, M, Brice, A, Nacmias, B, Sorbi, S, Bagnoli, S, Piaceri, I, Nielsen, Je, Hjermind, Le, Riemenschneider, M, Mayhaus, M, Ibach, B, Gasparoni, G, Pichler, S, Gu, W, Rossor, Mn, Fox, Nc, Warren, Jd, Grazia Spillantini, M, Morris, Hr, Rizzu, P, Heutink, P, Snowden, J, Rollinson, S, Richardson, A, Gerhard, A, Bruni, Ac, Maletta, R, Frangipane, F, Cupidi, C, Bernardi, L, Anfossi, M, Gallo, M, Elena Conidi, M, Smirne, N, Rademakers, R, Baker, M, Dickson, Dw, Graff-Radford, Nr, Petersen, Rc, Knopman, D, Josephs, Ka, Boeve, Bf, Parisi, Je, Seeley, Ww, Miller, Bl, Karydas, Am, Rosen, H, van Swieten, Jc, Dopper, Egp, Seelaar, H, Pijnenburg, Yal, Scheltens, P, Logroscino, G, Capozzo, R, Novelli, V, Puca, Aa, Franceschi, M, Postiglione, A, Milan, G, Sorrentino, P, Kristiansen, M, Chiang, Hh, Graff, C, Pasquier, F, Rollin, A, Deramecourt, V, Lebouvier, T, Kapogiannis, D, Ferrucci, L, Pickering-Brown, S, Singleton, Ab, Hardy, J, Momeni, P, and Int FTD-Genomics Consortium IFGC

Subjects
Male, Heterozygote, amyotrophic lateral sclerosis, Genotype, genetic association, Age of onset, Polymorphism, Single Nucleotide, frontotemporal dementia, age of onset, C9orf72, Humans, amyotrophic lateral sclerosi, Aged, C9orf72 Protein, Original Articles, DNA Methylation, Middle Aged, Amyotrophic lateral sclerosis, Gene Expression Regulation, Genetic association, CpG Islands, Female, Human medicine, Neurology (clinical), Frontotemporal dementia
Abstract

Discovery of disease age-of-onset modifiers is important for clinical trials and drug design. Zhang et al. perform a genome-wide analysis of epigenetic functional polymorphisms and identify an association between the C6orf10/LOC101929163 locus and age of FTD/ALS onset. The risk allele may be associated with a pro-inflammatory state in the brain., The G4C2-repeat expansion in C9orf72 is the most common known cause of amyotrophic lateral sclerosis and frontotemporal dementia. The high phenotypic heterogeneity of C9orf72 patients includes a wide range in age of onset, modifiers of which are largely unknown. Age of onset could be influenced by environmental and genetic factors both of which may trigger DNA methylation changes at CpG sites. We tested the hypothesis that age of onset in C9orf72 patients is associated with some common single nucleotide polymorphisms causing a gain or loss of CpG sites and thus resulting in DNA methylation alterations. Combined analyses of epigenetic and genetic data have the advantage of detecting functional variants with reduced likelihood of false negative results due to excessive correction for multiple testing in genome-wide association studies. First, we estimated the association between age of onset in C9orf72 patients (n = 46) and the DNA methylation levels at all 7603 CpG sites available on the 450 k BeadChip that are mapped to common single nucleotide polymorphisms. This was followed by a genetic association study of the discovery (n = 144) and replication (n = 187) C9orf72 cohorts. We found that age of onset was reproducibly associated with polymorphisms within a 124.7 kb linkage disequilibrium block tagged by top-significant variation, rs9357140, and containing two overlapping genes (LOC101929163 and C6orf10). A meta-analysis of all 331 C9orf72 carriers revealed that every A-allele of rs9357140 reduced hazard by 30% (P = 0.0002); and the median age of onset in AA-carriers was 6 years later than GG-carriers. In addition, we investigated a cohort of C9orf72 negative patients (n = 2634) affected by frontotemporal dementia and/or amyotrophic lateral sclerosis; and also found that the AA-genotype of rs9357140 was associated with a later age of onset (adjusted P = 0.007 for recessive model). Phenotype analyses detected significant association only in the largest subgroup of patients with frontotemporal dementia (n = 2142, adjusted P = 0.01 for recessive model). Gene expression studies of frontal cortex tissues from 25 autopsy cases affected by amyotrophic lateral sclerosis revealed that the G-allele of rs9357140 is associated with increased brain expression of LOC101929163 (a non-coding RNA) and HLA-DRB1 (involved in initiating immune responses), while the A-allele is associated with their reduced expression. Our findings suggest that carriers of the rs9357140 GG-genotype (linked to an earlier age of onset) might be more prone to be in a pro-inflammatory state (e.g. by microglia) than AA-carriers. Further, investigating the functional links within the C6orf10/LOC101929163/HLA-DRB1 pathway will be critical to better define age-dependent pathogenesis of frontotemporal dementia and amyotrophic lateral sclerosis.

Published
2018
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